On the chapter about Editable DataTable
we can find this :

This chapter includes recipes for:
    Reading the contents of the DataTable
    Filtering out null values
    Uploading data
    Determining which cell has changed 
    Adding or removing columns
    Adding or removing rows
    Clearable, deletable, renamable, and hideable colum

See #2700 for background, cross reference biopython/biopython#2833 (comment) e.g.

$ grep assertTrue *.py | grep "=="
common_BioSQL.py:        self.assertTrue(self.db.load(seqiter) == 1)
test_ClustalOmega_tool.py:        self.assertTrue(error.strip() == "" or
...

and:

$ grep assertFalse *.py | grep "!="
test_Restriction.py:        self

According to the conda build documentation and the referenced PEP-386 verlib, version numbers should not start with 'v'. This is violated in the following 13 recipes:

$ grep -R "{% set version *= *['\"]v"   . 
./recipes/perl-bio-viennangs/met

New feature

Ability to specify the Compute Engine disk type (pd-standard or local-SSD) found in the new Cloud Life Sciences API (https://cloud.google.com/life-sciences/docs/reference/rpc/google.cloud.lifesciences.v2beta#disk).

Usage scenario

Job's that require a high input/output operations per second and lower latency (https://cloud.google.com/compute/docs/disks/local-ssd).

S

I am planning a large alignment run on a non human species using a non alt aware reference.
I would like to determine which combination of BWA MEM "-M" and "-Y" options I should be using.
As far as I can tell "-M" used to be needed for the Picard compatibility as sometimes mentioned in the man page.

GATK 4 now recommends not to use "-M" for the human alt aware reference.
But they are now rec

Three very minor typos are present in these documents that break the code when copied-and-pasted as they are.

Link: https://gatk.broadinstitute.org/hc/en-us/community/posts/360056484652-Typos-in-docs

--

1.  https://gatk.broadinstitute.org/hc/en-us/articles/360036726571-LeftAlignAndTrimVariants

the fifth code block on this page

fastp will overwrite -o without checking if it is the same as -i. Worth adding a check for this scenario.

Add a new method:

proc.SetPathAuditHashed(portName string, prefix string, suffix string)

... which will create a SHA1(?) hash the port name plus all the command, parameters, and upstream commands and parameters used to create the specific file.

Usage example:

proc.SetPathAuditHashed("csvfile", "dat/", ".csv")

Internally, it should use a function, that can als

This would make the process for making small corrections easier for non-developers. From a comment on #8349.

This should be pretty easy to do and a good task for a new developer or community member looking to make a small contribution.

When seqtk sample requests more reads (integer argument) than there are reads in the input, the input is returned and no warnings are written to STDERR. Exit status is 0 (success).

This behavior may not be obvious to all users and I could not find it quickly in user docs. Please add this to the docs if this is in fact the intended behavior. Thank you!

Please consider mentioning explicitly in the documentation of scanpy.api.tl.diffmap that "the 0-th column is the steady-state solution, which is non-informative in diffusion maps", as mentioned here: https://github.com/theislab/single-cell-tutorial/blob/master/latest_notebook/Case-study_Mouse-intest

I tried to run Hail with Spark 2.4.4 built for Scala 2.12, and it did not work. It does work with Spark 2.4.4 built for Scala 2.11.

Here's the error I got with Scala 2.12:

Py4JJavaError: An error occurred while calling z:is.hail.HailContext.apply.
: java.lang.NoSuchMethodError: scala/Predef$.refArrayOps([Ljava/lang/Object;)Lscala/collection/mutable/ArrayOps; (loaded from file:/home/hammer

Hello old friends,

Galaxy has shipped v3.0.0a1 but links to the v2 docs as the v3 docs aren't being built:

https://github.com/galaxyproject/tools-iuc/blob/60e2302cfac90d0c909ef61815aaaafaaad5816a/tools/khmer/macros.xml#L2

https://github.com/galaxyproject/tools-iuc/blob/60e2302cfac90d0c909ef61815aaaafaaad5816a/tools/khmer/macros.xml#L92

https://khmer.readthedocs.io/en/v3.0.0a1/

Ch

By far the worst part of the docs is for Custom Content. This could do with a rewrite, with much more explicit instructions of what is possible and where to find more information about configuration and organisation.

Embedding lots of examples from the TestData repo will help people a lot I think.

First of all, thanks for creating scispacy, I think it's an amazing tool and very useful!!

I was running into an issue when saving the output of scispacy. I tried to pickle a Doc object, as explained on the website of spaCy, as follows:

import spacy
import pickle

nlp = spacy.load("en_core_sci_sm")

# add the Abbreviation Detector
abbrev

This codepen shows the issue: https://codepen.io/dylanvann/pen/OYaedz

The onHover handler forces a re-render.

Whenever the Plot is re-rendered some state is lost. In particular the selection is lost.

How it behaves when re-rendering (selection box is not maintained):

H

The graph action in womtool works fine, but when adding the --all argument, it gives the error:

java -jar womtool-44.jar --all graph host_workflow.wdl 
Error: Unknown option --all

Frequently, users insert figures incorrectly at biostars as they use a page link instead of a figure link. An enhancement can be made.

In the biostar/static/lib/pagedown/Markdown.Editor.js

1. Change
   `imagedialog: "

   Insert Image

   http://example.com/images/diagram.jpg "optional title"
   
   Need

The installation section currently says to use npm install --save circos with no further instruction.

Doing just this and then using Browserify to require circos results in the following error:
Error: Cannot find module '!!../../node_modules/css-loader/index.js!./tooltip.css' from '/.../node_modules/circos/dist'

Is there an assumption that Webpack is being used by those who try to impo

Dear @kblin,

I would like to use ncbi-gneome-download as a python module within my pipeline and I have been having problems to decipher the arguments to pass to the download call. I guess the readme and documentation is not up to date or I am missing something.

For example, I tried on the command line and it worked fine for me the following code:

ncbi-genome-download -s genbank -F fast